Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes
ok, I tried with an arbitrary value of kb for all the harmonic bonds (715) and the distances as they are in the crystal structure. There are 5 harmonic bonds with FE which I defined in the itp, but I am getting an error on one of them while doing position restrained MD for 50 ps. I tried with both the constraints = none / hbond , but getting the same error. (Here, I have turned on the temperature coupling as well) *The bond in molecule-type Protein_chain_A between atoms 4207 FE and 2546 NE2 has an estimated oscillational period of 7.9e-03 ps, which is less than 5 times the time step of 2.0e-03 ps. Maybe you forgot to change the constraints mdp option.* Can you please suggest where might be the problem? Thanks, Sucharita On Wed, Jun 18, 2014 at 7:54 PM, Justin Lemkul wrote: > > > On 6/18/14, 6:47 AM, sucharita dey wrote: > >> Thanks Justin. The OGA topology is now OK. But still the problem with the >> FE ion persists (very high force on it) during the minimization. >> Yes, I want to link the FE with its co-ordination atoms by simple harmonic >> (bond type 6), can you please tell what will be the value for kb (the >> force >> constant)? >> >> > No idea. If there are no vibrational data available for the interaction, > you're stuck with using some arbitrary value. That's actually somewhat > common when dealing with transition metals, because that's the least of > your worries when it comes to such species; MM representations of such > metals are very poor in general. > > -Justin > > > >> On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul wrote: >> >> >>> >>> On 6/13/14, 2:11 AM, sucharita dey wrote: >>> >>> Dear Users, I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG (N-OxalyGlycine) and crystal waters. I have generated the initial topology of OGA from PRODRG and incorporated it in the the forcefield gromos 53a6 and since the forcefield already has parametrs for ZN and FE, I had no problem in generating the *.itp files. I solvated the system and ran steep minimization for 1000 steps with emstep = 0.1 and emtol 1. Is the NOG topology sound? PRODRG has known problems getting charges >>> right, but building a suitable NOG topology from existing building blocks >>> is trivial. >>> >>> >>> It ran for ~80 steps and stopped. I checked the gro file generated, the >>> problem is around OGA and the FE, and the OGA is loosing its structure. I suspect it due to clashes, -- actually in the crystal structure 2 oxygens of OGA are in co-ordination with the FE (the FE being co-ordinated with 4 other atoms including one O from crystal water). Sounds like a potential topology issue. One simple test is to run NOG >>> in >>> vacuo then in a box of water to see if it is stable on its own, then deal >>> with it in the context of the full protein+ions. >>> >>> >>> I have not considered the FE co-ordination, can you please suggest how >>> to >>> do this or else please suggest if you feel the problem is elsewhere. Ion coordination is easily done with distance restraints or type-6 >>> harmonic connections. >>> >>> Below is the comment given after minimization stopped: >>> *Energy minimization has stopped, but the forces havenot converged to therequested precision Fmax < 1 (whichmay not be possible for your system). Itstoppedbecause the algorithm tried to make a new step whose sizewas toosmall, or there was no change in the energy sincelast step. Either way, weregard the minimization asconverged to within the available machineprecision,given your starting configuration and EM parameters.Double precision normally gives you higher accuracy, butthis is often notneeded for preparing to run moleculardynamics.writing lowest energy coordinates.Steepest Descents converged to machine precision in 84 steps,but did not reach the requested Fmax < 1.Potential Energy = -3.7139549e+08Maximum force = 7.7602650e+14 on atom 4207Norm of force = 3.6179670e+12* NOTE: the atom 4207 with maximum force is FE You have essentially infinite forces, which indicate very bad geometry, >>> clashes, or a bad topology. >>> >>> -Justin >>> >>> -- >>> == >>> >>> Justin A. Lemkul, Ph.D. >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow >>> >>> Department of Pharmaceutical Sciences >>> School of Pharmacy >>> Health Sciences Facility II, Room 601 >>> University of Maryland, Baltimore >>> 20 Penn St. >>> Baltimore, MD 21201 >>> >>> jalem...@outerbanks.umaryland.edu | (410) 706-7441 >>> http://mackerell.umaryland.edu/~jalemkul >>> >>> == >>> -- >>> Gromacs Users mailing list >>> >>> * Please search the archive at http://www.gromacs.org/ >>> Support/Maili
Re: [gmx-users] Atom was not found
If your protein is an oligomer, then you can check the termini of the monomers. After doing the pdb2gmx sometime GROMACS removes those 'TER' words at end of each monomers, so what you can do is retype 'TER' at the end of each monomers. This might help you. > Message: 1 > Date: Wed, 18 Jun 2014 10:30:14 -0400 > From: Justin Lemkul > To: gmx-us...@gromacs.org > Subject: Re: [gmx-users] Atom was not found > Message-ID: <53a1a276.7030...@vt.edu> > Content-Type: text/plain; charset=ISO-8859-1; format=flowed > > > On 6/18/14, 9:21 AM, h.aliza...@znu.ac.ir wrote: > Dear Users, > I want to simulate a protein by GROMACS. > When I use pdb2gmx command, topology and other files are produced from my > pdb file. > But when I define a box for my protein by editconf before pdb2gmx, I face > with this fatal error: > > "Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms > while sorting atoms" > > of course as I said, without defining a box, pdb2gmx is ok!! > > > Defining the box alone should have no effect on what the atoms are, unless > something has been renamed by changing formats or something. Do a diff on > the files before and after editconf, but there is no real reason why anything > > should > have been changed, or any real reason to manipulate the box before pdb2gmx. > -Justin -- With Regards Monoj Mon Kalita Taipei, Taiwan -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/18/14, 5:08 PM, Matthew Stancea wrote: After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing "None" for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter " and was asked about the protonation states for two of the residues, but I was not asked about the termini. Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? Coordinate file, always manipulate the coordinate file. But the fact that you're asking this tells me that likely you never actually added those prefixes, so pdb2gmx is being "smart" and adding them for you. In that case, there's nothing you can do short of (1) modifying the pdb2gmx code, (2) manually hacking the topology - ugly, but effective, or (3) using a different force field that doesn't have terminus-specific naming (anything that's not Amber). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. >>> You need to be using -ter and choosing "None" for both termini, otherwise >>> the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. >> I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o >> conf.gro -p topol.top -i posre.itp -inter -ter " and was asked about the protonation states for two of the residues, but I was not asked about the termini. >Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. Okay, which file do I remove the N and C prefixes from? -Matthew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/18/14, 4:53 PM, Matthew Stancea wrote: After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing "None" for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. -Justin I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter " and was asked about the protonation states for two of the residues, but I was not asked about the termini. Ah, because it's Amber. Amber force fields are special and have specific nomenclature that signifies N- and C-termini, so they automatically get built. Changing the residue names by removing the N and C prefixes should fix things. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
>> After editing the pdb only in the area of the names of the atoms (such as >> HB3), I was able to generate a topol.top file with a bond between the first >> nitrogen and the last carbon. However, I still have 2 too many hydrogens on >> the first nitrogen and 1 too many oxygens on the last carbon. >You need to be using -ter and choosing "None" for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. >-Justin I used the command "pdb2gmx_mpi -ff amber99sb -water tip3p -f 1NB1.pdb -o conf.gro -p topol.top -i posre.itp -inter -ter " and was asked about the protonation states for two of the residues, but I was not asked about the termini. -Matthew -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
On 6/18/14, 3:31 PM, Matthew Stancea wrote: Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. ie. do the replacement on your input coordinate file, not the .rtp! Mark Dr. Mark Abraham, My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, connected to that carbon (other than the alpha carbon) is the sulfur molecule. The only logical placement of for "HB3" is to that sulfur, except that the sulfur should not have any hydrogens bound to it since it is supposed form a disulfide bridge with another cysteine. Because of that, I am sure you can understand why I am scratching my head on this issue... HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and HB3 instead of HB1 and HB2, and the B means "beta"). Your description doesn't make any real sense to me. Visualize your structure. If you have a full set of protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the force field happy. If there is an HG on SG (the sulfur atom), then it will be deleted by pdb2gmx when you tell it to create a disulfide. -Justin My apologies! My description was not very clear, and now I see that. However, because you mentioned that HG would be the name of the hydrogen attached to the sulfur, I believe that perhaps changing the name of some of the hydrogens in the pdb file can fix the issue. After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. You need to be using -ter and choosing "None" for both termini, otherwise the default behavior takes over and pdb2gmx builds ionized termini. You don't have free termini, so you have to take control of pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Using specbond.dat in pdb2gmx
>>> Or observe that the .rtp entry has names like HB1 and HB2, rather than HB2 and HB3 and use sed (or your text editor) to do the replacement. >>> >>> ie. do the replacement on your input coordinate file, not the .rtp! >>> >>> Mark >> Dr. Mark Abraham, >> >> My pdb file contains HB1 and HB2 on a beta carbon of a cysteine. Well, >> connected to that carbon (other than the alpha carbon) is the sulfur >> molecule. The only logical placement of for "HB3" is to that sulfur, except >> that the sulfur should not have any hydrogens bound to it since it is >> supposed form a disulfide bridge with another cysteine. >> >> Because of that, I am sure you can understand why I am scratching my head on >> this issue... >HB3 is sometimes the nomenclature of beta carbons (some programs write HB2 and HB3 instead of HB1 and HB2, and the B means "beta"). Your description doesn't make any real sense to me. Visualize your structure. If you have a full set of protons on Cys, you should have HA, HB1, and HB2 on the side chain to make the force field happy. If there is an HG on SG (the sulfur atom), then it will be deleted by pdb2gmx when you tell it to create a disulfide. >-Justin My apologies! My description was not very clear, and now I see that. However, because you mentioned that HG would be the name of the hydrogen attached to the sulfur, I believe that perhaps changing the name of some of the hydrogens in the pdb file can fix the issue. After editing the pdb only in the area of the names of the atoms (such as HB3), I was able to generate a topol.top file with a bond between the first nitrogen and the last carbon. However, I still have 2 too many hydrogens on the first nitrogen and 1 too many oxygens on the last carbon. However, even with this small discrepancy, I am astounded that I was able to finally generate a conf.gro and topol.top of a cyclotide with a bond between the terminal N and the terminal C! Thank you so much for your help, Dr. Lemkul and Dr. Abraham! Matthew -Matthew Stancea -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] tunepme does not start
Indeed, it does some similar things, but the scope of the respective optimizations is different. Mark On Jun 18, 2014 5:39 PM, "Soren Wacker" wrote: > Then I misunderstood the function of -tunepme. > I thought it replaces g_tune_pme, but that is apparently not the case. > Thanks > Soren > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] genbox solvate insert_molecules
On 6/18/14, 1:52 PM, Soren Wacker wrote: Hi, when I start genbox with GMX5.x, I get the message: This tool has been removed from Gromacs 5.0. Please see http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at this website it is stated: "This tool has been split to gmx solvate and gmx insert-molecules." Apparently, these tools do not exist on my system. Should they be compiled by default? How can I generate these files if not? There is only one "gmx" binary that is installed in 5.0. Old tool names link to it and all commands (like "gmx solvate") are invoked as modules of gmx. Try "gmx solvate -h" and see if it works. It is installed by default. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] genbox solvate insert_molecules
Hi, when I start genbox with GMX5.x, I get the message: This tool has been removed from Gromacs 5.0. Please see http://www.gromacs.org/Documentation/How-tos/Tool_Changes_for_5.0 at this website it is stated: "This tool has been split to gmx solvate and gmx insert-molecules." Apparently, these tools do not exist on my system. Should they be compiled by default? How can I generate these files if not? best Soren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with Charmm36 ff
Thank you very much, Justin and Thomas, for your helpful effort!!! Best Regards > > > On 6/18/14, 11:45 AM, Thomas Piggot wrote: > > Apologies for any confusion over the naming of the downloadable files, they were > > originally made well before any modification to the protein parameters were > > published. Due to the way the CHARMM27 force field was named "charmm27.ff" but > > also included things you probably shouldn't call CHARMM27, like the protein > > force field which is (as you mentioned) CHARMM22 + CMAP, it made sense at the > > time to just call the force field "charmm36.ff". > > > > Anyway, I have just updated the description of the downloadable force field (on > > the user contribution section of the website) to make it clearer that it > > includes CHARMM36 for the lipids and CHARMM22 + CMAP for the protein. Hopefully > > this will alleviate any future confusion for people. > > > > Thanks, Tom. Much appreciated. The CHARMM27 issue is another good one. > Technically C27 is a nucleic acid force field, so it always gets a chuckle when > people publish proteins "simulated with C27." ;) > > -Justin > > > Cheers > > > > Tom > > > > On 18/06/14 16:19, Justin Lemkul wrote: > >> > >> > >> On 6/18/14, 11:03 AM, esteban.pedru...@uv.es wrote: > >>> Thanks, Justin. > >>> I will do it right now but, in the meantime, what do you think about the > >>> paper I mention? They use C36 for lipids an C22 for melittin, as I > >>> understand well. I am aware that they dont use Gromacs. If it is > >>> published that this ff "mix" works well... Maybe there is something I > >>> miss. > >>> Thank you very much again > >>> > >> > >> The problem is in the implementation of the force field, not necessarily the > >> force field itself. The C36 lipid parameters were developed alongside the > >> C22/CMAP implementation of proteins, and then later those C22/CMAP parameters > >> were further refined to yield the C36 protein force field. The atomtypes > >> implemented in the Gromacs version of C22/CMAP (under the charmm27.ff > >> directory) are named differently than the atomtypes in the C36 force field > >> (which we take directly from CHARMM). There is a hybrid C22/CMAP + C36 force > >> field available on the Gromacs downloads page that could rectify this > >> situation, but it is misleadingly named "CHARMM36," but in fact it is only C36 > >> lipids. > >> > >> In either case, we consider the C36 protein parameters superior to C22/CMAP, > >> but for the purposes of reproducing existing work I can understand why the > >> combination might still be useful. > >> > >> -Justin > >> > > > On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: > > Dear gmx users, > > I am trying to make MD for a DPPC bilayer with a melittin protein > >>> (pbd > > ID: 2MLT) positioned in the water slab, using Charmm36 ff for the > >>> lipids > > and Charmm22 for melittin, following this paper (Andersson, et all > > Biophysical Journal Volume 104 March 2013 L12–L14). The procedure > >>> is > > the following: > > 1) I go to Klauda web page > > (http://terpconnect.umd.edu/~jbklauda/research/download.html) and > > download the DPPC bilayer (pdb file), eliminate the water and make: > > pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all- atom > >>> force > > field, previously downloaded from charmm36-mar2014.ff from Charmm > > webpage, and tip3p water) > > > > 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing > >>> CHARMM27 > > all-atom force field (with CMAP) - version 2.0, and tip3p water) > > > > I merged the 2 .gro's and solvated and it is OK. However, when I go > >>> to > > add ions with grompp, I obtain the following error: > > > > -- > > Program grompp, VERSION 4.6.5 > > Source code file: /home/pedrueza/gromacs- 4.6.5/src/kernel/toppush.c, > > line: 1336 > > > > Fatal error: > > Atomtype HB not found > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > My topol.top file is this: (previously I modified the topol.top > >>> files to > > itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) > >>> and > > #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the > > [molecules], [system] and the other directives, like posre or ions > >>> itp) > > > > --- > > ; Include forcefield parameters > > #include "charmm36-mar2014.ff/forcefield.itp" > > > > ; Include chain topologies > > #include "dppc.itp" > > #include "2MLT.itp" > > > > ; Include water topology > > #include "charmm36-mar2014.ff/tip3p.itp" > > > > #ifdef POSRES_W
Re: [gmx-users] problem with Charmm36 ff
On 6/18/14, 11:45 AM, Thomas Piggot wrote: Apologies for any confusion over the naming of the downloadable files, they were originally made well before any modification to the protein parameters were published. Due to the way the CHARMM27 force field was named "charmm27.ff" but also included things you probably shouldn't call CHARMM27, like the protein force field which is (as you mentioned) CHARMM22 + CMAP, it made sense at the time to just call the force field "charmm36.ff". Anyway, I have just updated the description of the downloadable force field (on the user contribution section of the website) to make it clearer that it includes CHARMM36 for the lipids and CHARMM22 + CMAP for the protein. Hopefully this will alleviate any future confusion for people. Thanks, Tom. Much appreciated. The CHARMM27 issue is another good one. Technically C27 is a nucleic acid force field, so it always gets a chuckle when people publish proteins "simulated with C27." ;) -Justin Cheers Tom On 18/06/14 16:19, Justin Lemkul wrote: On 6/18/14, 11:03 AM, esteban.pedru...@uv.es wrote: Thanks, Justin. I will do it right now but, in the meantime, what do you think about the paper I mention? They use C36 for lipids an C22 for melittin, as I understand well. I am aware that they dont use Gromacs. If it is published that this ff "mix" works well... Maybe there is something I miss. Thank you very much again The problem is in the implementation of the force field, not necessarily the force field itself. The C36 lipid parameters were developed alongside the C22/CMAP implementation of proteins, and then later those C22/CMAP parameters were further refined to yield the C36 protein force field. The atomtypes implemented in the Gromacs version of C22/CMAP (under the charmm27.ff directory) are named differently than the atomtypes in the C36 force field (which we take directly from CHARMM). There is a hybrid C22/CMAP + C36 force field available on the Gromacs downloads page that could rectify this situation, but it is misleadingly named "CHARMM36," but in fact it is only C36 lipids. In either case, we consider the C36 protein parameters superior to C22/CMAP, but for the purposes of reproducing existing work I can understand why the combination might still be useful. -Justin On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: Dear gmx users, I am trying to make MD for a DPPC bilayer with a melittin protein (pbd ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids and Charmm22 for melittin, following this paper (Andersson, et all Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is the following: 1) I go to Klauda web page (http://terpconnect.umd.edu/~jbklauda/research/download.html) and download the DPPC bilayer (pdb file), eliminate the water and make: pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force field, previously downloaded from charmm36-mar2014.ff from Charmm webpage, and tip3p water) 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 all-atom force field (with CMAP) - version 2.0, and tip3p water) I merged the 2 .gro's and solvated and it is OK. However, when I go to add ions with grompp, I obtain the following error: -- Program grompp, VERSION 4.6.5 Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype HB not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topol.top file is this: (previously I modified the topol.top files to itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the [molecules], [system] and the other directives, like posre or ions itp) --- ; Include forcefield parameters #include "charmm36-mar2014.ff/forcefield.itp" ; Include chain topologies #include "dppc.itp" #include "2MLT.itp" ; Include water topology #include "charmm36-mar2014.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include Position restraint file #ifdef POSRES #include "posre_dppc.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre_2MLT.itp" #endif ; Include topology for ions #include "charmm36-mar2014.ff/ions.itp" [ system ] ; Name DPPC bilayer plus 2MLT in water [ molecules ] ; Compound#mols Other 72 Protein 1 SOL 4054 --- I think is a problem with nomenclature of atoms, but it is strange the mixing of the 2 forcefields??? Yes, it is. Use CHARMM36 for everything.
Re: [gmx-users] (no subject)
On 6/18/14, 11:43 AM, fatemeh ramezani wrote: Dear Users I run this command: nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr & Despite the use of nohup and &, mdrun will stop after closing the putty window. Can anyone help me to solve this problem? Google knows. Apparently nohup in Putty is a known problem. In any case, this is not a Gromacs problem, so you should be searching for solutions in more appropriate places. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Mdrun kill despite the use of nohup
Dear Users I run this command: nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr & Despite the use of nohup and &, mdrun will stop after closing the putty window. Can anyone help me to solve this problem? thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with Charmm36 ff
Apologies for any confusion over the naming of the downloadable files, they were originally made well before any modification to the protein parameters were published. Due to the way the CHARMM27 force field was named "charmm27.ff" but also included things you probably shouldn't call CHARMM27, like the protein force field which is (as you mentioned) CHARMM22 + CMAP, it made sense at the time to just call the force field "charmm36.ff". Anyway, I have just updated the description of the downloadable force field (on the user contribution section of the website) to make it clearer that it includes CHARMM36 for the lipids and CHARMM22 + CMAP for the protein. Hopefully this will alleviate any future confusion for people. Cheers Tom On 18/06/14 16:19, Justin Lemkul wrote: On 6/18/14, 11:03 AM, esteban.pedru...@uv.es wrote: Thanks, Justin. I will do it right now but, in the meantime, what do you think about the paper I mention? They use C36 for lipids an C22 for melittin, as I understand well. I am aware that they dont use Gromacs. If it is published that this ff "mix" works well... Maybe there is something I miss. Thank you very much again The problem is in the implementation of the force field, not necessarily the force field itself. The C36 lipid parameters were developed alongside the C22/CMAP implementation of proteins, and then later those C22/CMAP parameters were further refined to yield the C36 protein force field. The atomtypes implemented in the Gromacs version of C22/CMAP (under the charmm27.ff directory) are named differently than the atomtypes in the C36 force field (which we take directly from CHARMM). There is a hybrid C22/CMAP + C36 force field available on the Gromacs downloads page that could rectify this situation, but it is misleadingly named "CHARMM36," but in fact it is only C36 lipids. In either case, we consider the C36 protein parameters superior to C22/CMAP, but for the purposes of reproducing existing work I can understand why the combination might still be useful. -Justin On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: Dear gmx users, I am trying to make MD for a DPPC bilayer with a melittin protein (pbd ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids and Charmm22 for melittin, following this paper (Andersson, et all Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is the following: 1) I go to Klauda web page (http://terpconnect.umd.edu/~jbklauda/research/download.html) and download the DPPC bilayer (pdb file), eliminate the water and make: pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force field, previously downloaded from charmm36-mar2014.ff from Charmm webpage, and tip3p water) 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 all-atom force field (with CMAP) - version 2.0, and tip3p water) I merged the 2 .gro's and solvated and it is OK. However, when I go to add ions with grompp, I obtain the following error: -- Program grompp, VERSION 4.6.5 Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype HB not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topol.top file is this: (previously I modified the topol.top files to itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the [molecules], [system] and the other directives, like posre or ions itp) --- ; Include forcefield parameters #include "charmm36-mar2014.ff/forcefield.itp" ; Include chain topologies #include "dppc.itp" #include "2MLT.itp" ; Include water topology #include "charmm36-mar2014.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include Position restraint file #ifdef POSRES #include "posre_dppc.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre_2MLT.itp" #endif ; Include topology for ions #include "charmm36-mar2014.ff/ions.itp" [ system ] ; Name DPPC bilayer plus 2MLT in water [ molecules ] ; Compound#mols Other 72 Protein 1 SOL 4054 --- I think is a problem with nomenclature of atoms, but it is strange the mixing of the 2 forcefields??? Yes, it is. Use CHARMM36 for everything. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University
[gmx-users] (no subject)
Dear Users I run this command: nohup mpirun -np 8 mdrun_mpi -s x.tpr -o x.trr -c x.pdb -g x.log -e x.edr & Despite the use of nohup and &, mdrun will stop after closing the putty window. Can anyone help me to solve this problem? thank you in advance -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] tunepme does not start
Then I misunderstood the function of -tunepme. I thought it replaces g_tune_pme, but that is apparently not the case. Thanks Soren -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] pdb2gmx
On 6/18/14, 11:18 AM, mirko busato wrote: Dear Users, I am using the command pdb2gmx_d on a neutral peptide in this way: pdb2gmx_d -f pep2_n.pdb -water none -inter My force field is AMBER. The first residue is ASN and the last residue is ARG My terminals are not ionized (NH2 and COOH). So I changed the name of residue ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS in ACE for the 4 atoms (C,O2,O1,H2). If in the interactive way I select ARG (not protonated) ,I obtained a message like that " Fatal error: In the chosen force field there is no residue type for 'ARGN' ". After I tried to select ARG(protonated) and I obtained this error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues sothat they match the residue database (.rtp) entries, or provide terminal database entries (.tdb). Could you help me? If you have non-amino acids as the termini (i.e. capping groups), you need to select "None" for both termini. The side chain protonation is irrelevant to the treatment of the actual termini. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with Charmm36 ff
On 6/18/14, 11:03 AM, esteban.pedru...@uv.es wrote: Thanks, Justin. I will do it right now but, in the meantime, what do you think about the paper I mention? They use C36 for lipids an C22 for melittin, as I understand well. I am aware that they dont use Gromacs. If it is published that this ff "mix" works well... Maybe there is something I miss. Thank you very much again The problem is in the implementation of the force field, not necessarily the force field itself. The C36 lipid parameters were developed alongside the C22/CMAP implementation of proteins, and then later those C22/CMAP parameters were further refined to yield the C36 protein force field. The atomtypes implemented in the Gromacs version of C22/CMAP (under the charmm27.ff directory) are named differently than the atomtypes in the C36 force field (which we take directly from CHARMM). There is a hybrid C22/CMAP + C36 force field available on the Gromacs downloads page that could rectify this situation, but it is misleadingly named "CHARMM36," but in fact it is only C36 lipids. In either case, we consider the C36 protein parameters superior to C22/CMAP, but for the purposes of reproducing existing work I can understand why the combination might still be useful. -Justin On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: Dear gmx users, I am trying to make MD for a DPPC bilayer with a melittin protein (pbd ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids and Charmm22 for melittin, following this paper (Andersson, et all Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is the following: 1) I go to Klauda web page (http://terpconnect.umd.edu/~jbklauda/research/download.html) and download the DPPC bilayer (pdb file), eliminate the water and make: pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force field, previously downloaded from charmm36-mar2014.ff from Charmm webpage, and tip3p water) 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 all-atom force field (with CMAP) - version 2.0, and tip3p water) I merged the 2 .gro's and solvated and it is OK. However, when I go to add ions with grompp, I obtain the following error: -- Program grompp, VERSION 4.6.5 Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype HB not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topol.top file is this: (previously I modified the topol.top files to itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the [molecules], [system] and the other directives, like posre or ions itp) --- ; Include forcefield parameters #include "charmm36-mar2014.ff/forcefield.itp" ; Include chain topologies #include "dppc.itp" #include "2MLT.itp" ; Include water topology #include "charmm36-mar2014.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include Position restraint file #ifdef POSRES #include "posre_dppc.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre_2MLT.itp" #endif ; Include topology for ions #include "charmm36-mar2014.ff/ions.itp" [ system ] ; Name DPPC bilayer plus 2MLT in water [ molecules ] ; Compound#mols Other 72 Protein 1 SOL 4054 --- I think is a problem with nomenclature of atoms, but it is strange the mixing of the 2 forcefields??? Yes, it is. Use CHARMM36 for everything. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Esteban Pedrueza Villalmanzo e-mails: esteban.pedru...@uv.es espevi1...@hotmail.com -- == Justin A. Lem
[gmx-users] pdb2gmx
Dear Users, I am using the command pdb2gmx_d on a neutral peptide in this way: pdb2gmx_d -f pep2_n.pdb -water none -inter My force field is AMBER. The first residue is ASN and the last residue is ARG My terminals are not ionized (NH2 and COOH). So I changed the name of residue ASN in NME for the 3 atoms (N,NH2,NH1), and I changed the name of residue LYS in ACE for the 4 atoms (C,O2,O1,H2). If in the interactive way I select ARG (not protonated) ,I obtained a message like that " Fatal error: In the chosen force field there is no residue type for 'ARGN' ". After I tried to select ARG(protonated) and I obtained this error: There is a dangling bond at at least one of the terminal ends and the force field does not provide terminal entries or files. Fix your terminal residues so that they match the residue database (.rtp) entries, or provide terminal database entries (.tdb). Could you help me? Thank you very much, Mirko -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with Charmm36 ff
Thanks, Justin. I will do it right now but, in the meantime, what do you think about the paper I mention? They use C36 for lipids an C22 for melittin, as I understand well. I am aware that they dont use Gromacs. If it is published that this ff "mix" works well... Maybe there is something I miss. Thank you very much again > > > On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: > > Dear gmx users, > > I am trying to make MD for a DPPC bilayer with a melittin protein (pbd > > ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids > > and Charmm22 for melittin, following this paper (Andersson, et all > > Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is > > the following: > > 1) I go to Klauda web page > > (http://terpconnect.umd.edu/~jbklauda/research/download.html) and > > download the DPPC bilayer (pdb file), eliminate the water and make: > > pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force > > field, previously downloaded from charmm36-mar2014.ff from Charmm > > webpage, and tip3p water) > > > > 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 > > all-atom force field (with CMAP) - version 2.0, and tip3p water) > > > > I merged the 2 .gro's and solvated and it is OK. However, when I go to > > add ions with grompp, I obtain the following error: > > > > -- > > Program grompp, VERSION 4.6.5 > > Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, > > line: 1336 > > > > Fatal error: > > Atomtype HB not found > > For more information and tips for troubleshooting, please check the > > GROMACS > > website at http://www.gromacs.org/Documentation/Errors > > --- > > > > My topol.top file is this: (previously I modified the topol.top files to > > itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and > > #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the > > [molecules], [system] and the other directives, like posre or ions itp) > > > > --- > > ; Include forcefield parameters > > #include "charmm36-mar2014.ff/forcefield.itp" > > > > ; Include chain topologies > > #include "dppc.itp" > > #include "2MLT.itp" > > > > ; Include water topology > > #include "charmm36-mar2014.ff/tip3p.itp" > > > > #ifdef POSRES_WATER > > ; Position restraint for each water oxygen > > [ position_restraints ] > > ; i funct fcxfcyfcz > > 11 1000 1000 1000 > > #endif > > > > > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre_dppc.itp" > > #endif > > > > ; Include Position restraint file > > #ifdef POSRES > > #include "posre_2MLT.itp" > > #endif > > > > ; Include topology for ions > > #include "charmm36-mar2014.ff/ions.itp" > > > > [ system ] > > ; Name > > DPPC bilayer plus 2MLT in water > > > > [ molecules ] > > ; Compound#mols > > Other 72 > > Protein 1 > > SOL 4054 > > --- > > > > I think is a problem with nomenclature of atoms, but it is strange the > > mixing of the 2 forcefields??? > > Yes, it is. Use CHARMM36 for everything. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. > -- Esteban Pedrueza Villalmanzo e-mails: esteban.pedru...@uv.es espevi1...@hotmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
Please keep the discussion on the gmx-users list. On 6/18/14, 9:10 AM, Amninder wrote: My mistake for subtraction but still too far from expt Value. I am using OPLS force field and parameters from virtual chemistry.org and used conditions corresponding to their paper. Post your .mdp files and perhaps we can spot anything that may not be correct. -Justin Sent from my iPhone On 18-Jun-2014, at 9:50 PM, Justin Lemkul wrote: On 6/18/14, 1:04 AM, AMNINDER SINGH wrote: Dear People, I am trying to calculate enthalpy of vaporization of methanol. Using energy –nmol on equilibrated methanol, E pot comes -5.005 KJ/mol. Then for EPot (gas) I got 14.405 KJ/mol. Using DHvap = Epot(gas) - Epot (liquid)+RT. My value comes around 11 KJ/mol much less than experimental value 37.43. Any idea where is mistake might be. It looks like the subtraction you did was incorrect, so your result ends up being about 22 kJ/mol, assuming T = 298 K (RT = 2.478). Is your force field model expected to reproduce the enthalpy of vaporization? Where did you get the parameters? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Atom was not found
On 6/18/14, 9:21 AM, h.aliza...@znu.ac.ir wrote: Dear Users, I want to simulate a protein by GROMACS. When I use pdb2gmx command, topology and other files are produced from my pdb file. But when I define a box for my protein by editconf before pdb2gmx, I face with this fatal error: "Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms while sorting atoms" of course as I said, without defining a box, pdb2gmx is ok!! Defining the box alone should have no effect on what the atoms are, unless something has been renamed by changing formats or something. Do a diff on the files before and after editconf, but there is no real reason why anything should have been changed, or any real reason to manipulate the box before pdb2gmx. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] problem with Charmm36 ff
On 6/18/14, 10:25 AM, esteban.pedru...@uv.es wrote: Dear gmx users, I am trying to make MD for a DPPC bilayer with a melittin protein (pbd ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids and Charmm22 for melittin, following this paper (Andersson, et all Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is the following: 1) I go to Klauda web page (http://terpconnect.umd.edu/~jbklauda/research/download.html) and download the DPPC bilayer (pdb file), eliminate the water and make: pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force field, previously downloaded from charmm36-mar2014.ff from Charmm webpage, and tip3p water) 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 all-atom force field (with CMAP) - version 2.0, and tip3p water) I merged the 2 .gro's and solvated and it is OK. However, when I go to add ions with grompp, I obtain the following error: -- Program grompp, VERSION 4.6.5 Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype HB not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topol.top file is this: (previously I modified the topol.top files to itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the [molecules], [system] and the other directives, like posre or ions .itp) --- ; Include forcefield parameters #include "charmm36-mar2014.ff/forcefield.itp" ; Include chain topologies #include "dppc.itp" #include "2MLT.itp" ; Include water topology #include "charmm36-mar2014.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include Position restraint file #ifdef POSRES #include "posre_dppc.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre_2MLT.itp" #endif ; Include topology for ions #include "charmm36-mar2014.ff/ions.itp" [ system ] ; Name DPPC bilayer plus 2MLT in water [ molecules ] ; Compound#mols Other 72 Protein 1 SOL 4054 --- I think is a problem with nomenclature of atoms, but it is strange the mixing of the 2 forcefields??? Yes, it is. Use CHARMM36 for everything. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] problem with Charmm36 ff
Dear gmx users, I am trying to make MD for a DPPC bilayer with a melittin protein (pbd ID: 2MLT) positioned in the water slab, using Charmm36 ff for the lipids and Charmm22 for melittin, following this paper (Andersson, et all Biophysical Journal Volume 104 March 2013 L12–L14). The procedure is the following: 1) I go to Klauda web page (http://terpconnect.umd.edu/~jbklauda/research/download.html) and download the DPPC bilayer (pdb file), eliminate the water and make: pdb2gmx -f bilayer.pdb -o bilayer.gro (choosing CHARMM36 all-atom force field, previously downloaded from charmm36-mar2014.ff from Charmm webpage, and tip3p water) 2)for the melittin: pdb2gmx -f 2MLT.pdb -o 2MLT.gro (choosing CHARMM27 all-atom force field (with CMAP) - version 2.0, and tip3p water) I merged the 2 .gro's and solvated and it is OK. However, when I go to add ions with grompp, I obtain the following error: -- Program grompp, VERSION 4.6.5 Source code file: /home/pedrueza/gromacs-4.6.5/src/kernel/toppush.c, line: 1336 Fatal error: Atomtype HB not found For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- My topol.top file is this: (previously I modified the topol.top files to itp simply erasing the #include "charmm27.ff/forcefield.itp" (2MLT) and #include "charmm36-mar2014.ff/forcefield.itp" (dppc), besides the [molecules], [system] and the other directives, like posre or ions .itp) --- ; Include forcefield parameters #include "charmm36-mar2014.ff/forcefield.itp" ; Include chain topologies #include "dppc.itp" #include "2MLT.itp" ; Include water topology #include "charmm36-mar2014.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcxfcyfcz 11 1000 1000 1000 #endif ; Include Position restraint file #ifdef POSRES #include "posre_dppc.itp" #endif ; Include Position restraint file #ifdef POSRES #include "posre_2MLT.itp" #endif ; Include topology for ions #include "charmm36-mar2014.ff/ions.itp" [ system ] ; Name DPPC bilayer plus 2MLT in water [ molecules ] ; Compound#mols Other 72 Protein 1 SOL 4054 --- I think is a problem with nomenclature of atoms, but it is strange the mixing of the 2 forcefields??? I am new in GMX so any help is highly appreciated. If you need I can provide the rest of files E. -- Esteban Pedrueza Villalmanzo e-mails: esteban.pedru...@uv.es espevi1...@hotmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] Atom was not found
Dear Users, I want to simulate a protein by GROMACS. When I use pdb2gmx command, topology and other files are produced from my pdb file. But when I define a box for my protein by editconf before pdb2gmx, I face with this fatal error: "Atom OXT in residue VAL 226 was not found in rtp entry VAL with 8 atoms while sorting atoms" of course as I said, without defining a box, pdb2gmx is ok!! Thanks for any help, Hadi -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp
On 6/18/14, 8:20 AM, Meenakshi Rajput wrote: Hi I have made my ligand coordinate file using prodrg server. And the 15 missing atoms are the ligand atoms as they are not seen in gro file. I have modified protein's topology file. Is there any change i have to make in gro file except adding ligand coordinates? Follow this protocol: http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html You'll undoubtedly need to correct the PRODRG topology (I probably say that at least once a week). -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp
Hi I have made my ligand coordinate file using prodrg server. And the 15 missing atoms are the ligand atoms as they are not seen in gro file. I have modified protein's topology file. Is there any change i have to make in gro file except adding ligand coordinates? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes
On 6/18/14, 6:47 AM, sucharita dey wrote: Thanks Justin. The OGA topology is now OK. But still the problem with the FE ion persists (very high force on it) during the minimization. Yes, I want to link the FE with its co-ordination atoms by simple harmonic (bond type 6), can you please tell what will be the value for kb (the force constant)? No idea. If there are no vibrational data available for the interaction, you're stuck with using some arbitrary value. That's actually somewhat common when dealing with transition metals, because that's the least of your worries when it comes to such species; MM representations of such metals are very poor in general. -Justin On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul wrote: On 6/13/14, 2:11 AM, sucharita dey wrote: Dear Users, I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG (N-OxalyGlycine) and crystal waters. I have generated the initial topology of OGA from PRODRG and incorporated it in the the forcefield gromos 53a6 and since the forcefield already has parametrs for ZN and FE, I had no problem in generating the *.itp files. I solvated the system and ran steep minimization for 1000 steps with emstep = 0.1 and emtol 1. Is the NOG topology sound? PRODRG has known problems getting charges right, but building a suitable NOG topology from existing building blocks is trivial. It ran for ~80 steps and stopped. I checked the gro file generated, the problem is around OGA and the FE, and the OGA is loosing its structure. I suspect it due to clashes, -- actually in the crystal structure 2 oxygens of OGA are in co-ordination with the FE (the FE being co-ordinated with 4 other atoms including one O from crystal water). Sounds like a potential topology issue. One simple test is to run NOG in vacuo then in a box of water to see if it is stable on its own, then deal with it in the context of the full protein+ions. I have not considered the FE co-ordination, can you please suggest how to do this or else please suggest if you feel the problem is elsewhere. Ion coordination is easily done with distance restraints or type-6 harmonic connections. Below is the comment given after minimization stopped: *Energy minimization has stopped, but the forces havenot converged to therequested precision Fmax < 1 (whichmay not be possible for your system). Itstoppedbecause the algorithm tried to make a new step whose sizewas toosmall, or there was no change in the energy sincelast step. Either way, weregard the minimization asconverged to within the available machineprecision,given your starting configuration and EM parameters.Double precision normally gives you higher accuracy, butthis is often notneeded for preparing to run moleculardynamics.writing lowest energy coordinates.Steepest Descents converged to machine precision in 84 steps,but did not reach the requested Fmax < 1.Potential Energy = -3.7139549e+08Maximum force = 7.7602650e+14 on atom 4207Norm of force = 3.6179670e+12* NOTE: the atom 4207 with maximum force is FE You have essentially infinite forces, which indicate very bad geometry, clashes, or a bad topology. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/ Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] min in vacuum
On 6/18/14, 5:08 AM, Urszula Uciechowska wrote: Hi gromacs users, I am trying to run coarse-grained MD for a protein system using martini protocol. First step is to run short min in vacuum, whenever I try to do this I am getting an error regarding my input file. ERROR 1 [file system-vaccum.top, line 16]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 note --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "I Caught It In the Face" (P.J. Harvey) My input file: integrator = steep dt = 0.02 nsteps = 10 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout= 100 xtc-precision= 10 rlist= 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r= 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein tau-t= 1.0 ref-t= 300 How should I modify it? Probably your box is too small. You haven't set the "pbc" keyword, so it defaults to "xyz," which is not really a vacuum system and will cause problems if the box is not of sufficient size. Note that the temperature settings and dt are ignored for EM. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp
On 6/18/14, 3:02 AM, Meenakshi Rajput wrote: Hi gromacs users I run the grompp command (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top) to generate .tpr file but i got the following error Fatal error: number of coordinates in coordinate file (sol.gro, 140012) does not match topology (hsa.top, 140027) When I opened gro file, only protein and sol molecules are seen in .gro file but no ligand molecules. I dont know why it is happening.. Can anybody help me? Not really. You haven't said how you've been keeping track of the system's contents or how you've constructed the coordinate file. You're missing 15 atoms somewhere - does that correspond to the ligand? Did you modify the coordinate file in some way? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] (no subject)
On 6/18/14, 1:04 AM, AMNINDER SINGH wrote: Dear People, I am trying to calculate enthalpy of vaporization of methanol. Using energy –nmol on equilibrated methanol, E pot comes -5.005 KJ/mol. Then for EPot (gas) I got 14.405 KJ/mol. Using DHvap = Epot(gas) - Epot (liquid)+RT. My value comes around 11 KJ/mol much less than experimental value 37.43. Any idea where is mistake might be. It looks like the subtraction you did was incorrect, so your result ends up being about 22 kJ/mol, assuming T = 298 K (RT = 2.478). Is your force field model expected to reproduce the enthalpy of vaporization? Where did you get the parameters? -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] CHARMM36 and carbohydrates
On 6/17/14, 11:26 PM, Timothy Click wrote: Greetings from Taiwan. I am having a bit of trouble setting up a carbohydrate in Gromacs. I have a PDB file that has a glucan chain between a graphene bilayer, but when I run pdb2gmx, it complains of missing atoms. Yes, an oxygen is supposed to be missing because of the 1,4 beta glycosyl linkage. I want to use the CHARMM36 force field, which has the individual carbohydrate defined. If I use CHARMM, I have no problem setting this up (initially setup to use NAMD), but I prefer Gromacs. Indeed, this is a known problem/limitation since CHARMM applies patches when piecing together oligosaccharides. Gromacs doesn't do that. The only way (at present) to do this entirely within Gromacs is to define your oligosaccharide as its own residue in the .rtp file. I believe someone (Roland?) mentioned a Python script that could patch things together, but that's the only workaround that I know of. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] peculiar water behavior
On 6/17/14, 5:20 PM, Chetan Mahajan wrote: Thanks, Justin. That makes it clear. I have one small question: I do not know how does position restraint algorithm work with other things in gromacs, but doesn't it generate a lot of stress due to slab moving from center to near box boundary despite of position restraints, when -com option is used for refcoord-scaling? If there is a lot of stress, would this stress affect simulation results? You can get a sense of that by extracting the energy associated with the restraints from the .edr file. -Justin -- == Justin A. Lemkul, Ph.D. Ruth L. Kirschstein NRSA Postdoctoral Fellow Department of Pharmaceutical Sciences School of Pharmacy Health Sciences Facility II, Room 601 University of Maryland, Baltimore 20 Penn St. Baltimore, MD 21201 jalem...@outerbanks.umaryland.edu | (410) 706-7441 http://mackerell.umaryland.edu/~jalemkul == -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Problem in energy minimization and further dynamics probably for atomic clashes
Thanks Justin. The OGA topology is now OK. But still the problem with the FE ion persists (very high force on it) during the minimization. Yes, I want to link the FE with its co-ordination atoms by simple harmonic (bond type 6), can you please tell what will be the value for kb (the force constant)? On Fri, Jun 13, 2014 at 8:41 PM, Justin Lemkul wrote: > > > On 6/13/14, 2:11 AM, sucharita dey wrote: > >> Dear Users, >> >> I have a protein-DNA system with 3 Zinc fingers, 1 Fe++, 1 cofactor NOG >> (N-OxalyGlycine) and crystal waters. >> >> I have generated the initial topology of OGA from PRODRG and incorporated >> it in the the forcefield gromos 53a6 and since the forcefield already has >> parametrs for ZN and FE, I had no problem in generating the *.itp files. >> I >> solvated the system and ran steep minimization for 1000 steps with emstep >> = >> 0.1 and emtol 1. >> >> > Is the NOG topology sound? PRODRG has known problems getting charges > right, but building a suitable NOG topology from existing building blocks > is trivial. > > > It ran for ~80 steps and stopped. I checked the gro file generated, the >> problem is around OGA and the FE, and the OGA is loosing its structure. I >> suspect it due to clashes, -- actually in the crystal structure 2 oxygens >> of OGA are in co-ordination with the FE (the FE being co-ordinated with 4 >> other atoms including one O from crystal water). >> >> > Sounds like a potential topology issue. One simple test is to run NOG in > vacuo then in a box of water to see if it is stable on its own, then deal > with it in the context of the full protein+ions. > > > I have not considered the FE co-ordination, can you please suggest how to >> do this or else please suggest if you feel the problem is elsewhere. >> >> > Ion coordination is easily done with distance restraints or type-6 > harmonic connections. > > Below is the comment given after minimization stopped: >> >> *Energy minimization has stopped, but the forces havenot converged to >> therequested precision Fmax < 1 (whichmay not be possible for your >> system). >> Itstoppedbecause the algorithm tried to make a new step whose sizewas >> toosmall, or there was no change in the energy sincelast step. Either way, >> weregard the minimization asconverged to within the available >> machineprecision,given your starting configuration and EM >> parameters.Double >> >> precision normally gives you higher accuracy, butthis is often notneeded >> for preparing to run moleculardynamics.writing lowest energy >> coordinates.Steepest Descents converged to machine precision in 84 >> steps,but did not reach the requested Fmax < 1.Potential Energy = >> -3.7139549e+08Maximum force = 7.7602650e+14 on atom 4207Norm of >> force = 3.6179670e+12* >> >> NOTE: the atom 4207 with maximum force is FE >> >> > You have essentially infinite forces, which indicate very bad geometry, > clashes, or a bad topology. > > -Justin > > -- > == > > Justin A. Lemkul, Ph.D. > Ruth L. Kirschstein NRSA Postdoctoral Fellow > > Department of Pharmaceutical Sciences > School of Pharmacy > Health Sciences Facility II, Room 601 > University of Maryland, Baltimore > 20 Penn St. > Baltimore, MD 21201 > > jalem...@outerbanks.umaryland.edu | (410) 706-7441 > http://mackerell.umaryland.edu/~jalemkul > > == > -- > Gromacs Users mailing list > > * Please search the archive at http://www.gromacs.org/ > Support/Mailing_Lists/GMX-Users_List before posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] grompp
Hi, Did you update the 2nd line of your gro file (sol.gro) after adding ligand coordinates? On Wed, Jun 18, 2014 at 12:32 PM, Meenakshi Rajput wrote: > Hi gromacs users > I run the grompp command > (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top) > to generate .tpr file but i got the following error > Fatal error: > number of coordinates in coordinate file (sol.gro, 140012) > does not match topology (hsa.top, 140027) > When I opened gro file, only protein and sol molecules are seen in .gro > file but no ligand molecules. I dont know why it is happening.. > Can anybody help me? > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- With Best Wishes Venkat Reddy Chirasani PhD student Laboratory of Computational Biophysics Department of Biotechnology IIT Madras Chennai INDIA-600036 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] min in vacuum
Hi gromacs users, I am trying to run coarse-grained MD for a protein system using martini protocol. First step is to run short min in vacuum, whenever I try to do this I am getting an error regarding my input file. ERROR 1 [file system-vaccum.top, line 16]: ERROR: The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist. There was 1 note --- Program grompp, VERSION 4.5.3 Source code file: grompp.c, line: 1356 Fatal error: There was 1 error in input file(s) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors --- "I Caught It In the Face" (P.J. Harvey) My input file: integrator = steep dt = 0.02 nsteps = 10 nstxout = 0 nstvout = 0 nstlog = 100 nstxtcout= 100 xtc-precision= 10 rlist= 1.4 coulombtype = shift rcoulomb = 1.2 epsilon_r= 15 vdw-type = shift rvdw-switch = 0.9 rvdw = 1.2 tcoupl = v-rescale tc-grps = Protein tau-t= 1.0 ref-t= 300 How should I modify it? Thank you in advance for any suggestions. best regards Urszula - Ta wiadomość została wysłana z serwera Uniwersytetu Gdańskiego http://www.ug.edu.pl/ -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] g_mmpbsa: MM-PBSA method for GROMACS
Thanks Rashmi. Finally, I have been able to install g_mmpbsa. Apart from the gmx lib files there were issues in installing APBS as well, took a quite amount of time to find the source code of that version that has the lib files needed for g_mmpbsa. Thanks anyways, Sucharita On Mon, Jun 16, 2014 at 9:39 PM, Rashmi wrote: > Hi Sucharita, > > Please post as new thread or in g_mmpbsa forum. > > You could install Gromacs at new location using followings with cmake: > > -DCMAKE_INSTALL_PREFIX=/to/custom/path > -DBUILD_SHARED_LIBS=OFF > -DGMX_GPU=off > > Then, g_mmpbsa can be compiled using this Gromacs. We will fix this > installation issue in future version. > > > > With Regards, > Rashmi > > > > On Mon, Jun 16, 2014 at 11:41 AM, sucharita dey > wrote: > > > Hi Rashmi, > > > > I am facing difficulty in installing the tool you mentioned g_mmpbsa. I > am > > giving this command: > > ./configure --enable-gmx46 --with-gmx-include=/usr/local/gromacs/include > > --with-gmx-lib=/usr/local/gromacs/lib > > > > configure: error: Could not find /libgmx.a library file > > > > I found in my gromacs4.6.3 lib folder '/usr/local/gromacs/lib' the files > > are 'libgmx.so', 'libgmxana.so' etc.. instead of 'libgmx.a' or > > 'libgmxana.a'. > > Please suggest how do I get this files without hampering my installed > > gromacs as presently a number of programs are running. > > > > Thanks, > > Sucharita > > > > > > On Fri, Jun 13, 2014 at 10:32 PM, Rashmi wrote: > > > > > Dear Prof. David van der Spoel, > > > > > > Thank you very much for considering g_mmpbsa for the GROMACS > repository. > > We > > > have a discussion on the same and will try to patch g_mmpbsa in the > > > repository. Presently, we do not know how to integrate compilation > > > procedure of g_mmpbsa with the GROMACS package as APBS libraries are > > > required during compilation and Fortran compiler are required for the > > > linking. > > > > > > Since I am travelling these days, hope we could able to work on the > same > > in > > > a month and so. > > > > > > With Regards > > > Rashmi Kumari > > > PhD Student > > > School of Computational and Integrative Sciences > > > Jawaharlal Nehru University > > > New Delhi, India. > > > > > > > > > > > > > > > > > > On Tue, Jun 10, 2014 at 1:42 AM, David van der Spoel < > > sp...@xray.bmc.uu.se > > > > > > > wrote: > > > > > > > On 2014-06-09 21:17, Rashmi wrote: > > > > > > > >> Dear GROMACS users, > > > >> > > > >> We have developed a new tool, > > > >> *g_mmpbsa* for GROMACS to carry out the MM-PBSA calculations. It > > uses > > > >> APBS libraries for the Poisson-Boltzmann calculations. > > > >> > > > >> > > > >> Features: > > > >> > > > >> - > > > >> Include SASA, SAV and WCA > > > >> -like > > > >> non-polar models > > > >> - It inherits threading (OpenMP) functions from APBS > > > >> - Simultaneously calculate > > > >> > > > >> energy contribution > > > >> s > > > >> of residue > > > >> s > > > >> to binding > > > >> > > > >> > > > >> > > > >> Details of this > > > >> tool > > > >> are given in the following link: > > > >> > > > >> http://rashmikumari.github.io/g_mmpbsa/ > > > >> > > > >> Its implementation and testing are discussed in the following > > > publication: > > > >> > > > >> http://pubs.acs.org/doi/abs/10.1021/ci500020m > > > >> > > > >> We would appreciate for suggestions > > > >> > > > >> regarding > > > >> > > > >> improvment of > > > >> > > > >> this tool. > > > >> > > > >> With Regards, > > > >> Rashmi > > > >> > > > >> Kumari > > > >> School of Computational and Integrative Sciences, > > > >> Jawaharlal Nehru University, > > > >> New Delhi > > > >> > > > >> 110067, India. > > > >> > > > >> Why not upload a patch to http://gerrit.gromacs.org ? > > > > > > > > > > > > -- > > > > David van der Spoel, Ph.D., Professor of Biology > > > > Dept. of Cell & Molec. Biol., Uppsala University. > > > > Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. > > > > sp...@xray.bmc.uu.sehttp://folding.bmc.uu.se > > > > -- > > > > Gromacs Users mailing list > > > > > > > > * Please search the archive at http://www.gromacs.org/ > > > > Support/Mailing_Lists/GMX-Users_List before posting! > > > > > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > > > > * For (un)subscribe requests visit > > > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users > or > > > > send a mail to gmx-users-requ...@gromacs.org. > > > > > > > > > > > > > > > > -- > > > With Regards, > > > > > > Rashmi Kumari > > > Visting Student > > > School of Chemistry and Molecular Biosciences (MD group) > > > The University of Queensland > > > St. Lucia, Brisbane, QLD 4072, Australia > > > Contact No.- +61 434872368. > > > -- > > > Gromacs Users mailing list > > > > > > * Please search the archive at > > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > > po
[gmx-users] Regarding the difference between g_dipoles and g_dielectric calculations
Hi All, Can someone give me some insights regarding the context under which we use the g_dipoles or g_dielectric (as mentioned below the two possible way of calculating dielectric constant) to calculate the dielectric constant of some molecule during simulation. g_dipoles computes the total dipole plus fluctuations of a simulation system. >From this you can compute e.g. the dielectric constant for low-dielectric media. g_dielectric calculates frequency dependent dielectric constants from the autocorrelation function of the total dipole moment. Thanks and Regards, Bipin Singh -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
[gmx-users] grompp
Hi gromacs users I run the grompp command (grompp_d -v -f minim.mdp -c sol.gro -o min.tpr -p hsa.top) to generate .tpr file but i got the following error Fatal error: number of coordinates in coordinate file (sol.gro, 140012) does not match topology (hsa.top, 140027) When I opened gro file, only protein and sol molecules are seen in .gro file but no ligand molecules. I dont know why it is happening.. Can anybody help me? -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
